Biotechnology in the Classroom: Using Genomics & Proteomics to ...

igocheddarBiotechnology

Dec 14, 2012 (4 years and 6 months ago)

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Biotechnology 101



Presented by Kristin Majda

kmajda@yahoo.com

Kristin Majda

Education


BS Biology & Minor in Professional Writing, U.C. Santa Barbara (1997)


Single Subject Clear Credential with CLAD, Cal State Northridge (2005)


MS Biotechnology & MBA, Cal State Channel Islands (2009)

Experience


Technical Writer (1997
-
2001)


Ventura County High School Science Teacher (2001
-
2009)


Oxnard College Instructor: Biology, Microbiology (2010)


CIRM Grant Analyst at Cal State Channel Islands (present)


VP of Gold Coast Science Network (GCSN), Member of Operating
Council for the Discovery Center for Science and Technology,

Member of AAAS, CA PTA Officer



About the Presenter

Introduction

This presentation intends to:


Introduce teachers to excellent resources for understanding and teaching
genetics and biotechnology (and their interconnection with molecular
and cellular biology, biochemistry, physiology, and evolution)


Provide a
very basic

introduction to the common biotechnologies
teachers may address in their courses




This workshop is NOT for individuals who already have a strong
understanding of biotechnology principles and are looking to
advance their knowledge.


Biotechnology 101

Introduction


Why is it important to include biotechnology in the K
-
12
science curriculum?


Biotechnology combines disciplines like genetics, molecular biology,
biochemistry, embryology and cell biology; with applications in medicine,
agriculture, environmental science, materials science, bio
-
fuels, etc.


Jobs in the biotechnology sector are increasing and there is a critical need for
a vast range of skilled workers, from lab assistants to PhD researchers


Biology and chemistry teachers can use applications of biotechnology to
strongly engage student interest and stimulate student
-
directed investigation
and experimentation in their classrooms


Biotechnology is part of the CA science standards for high school biology,
but has applications to many standards across the sciences for all grade
levels


Biotechnology 101

Introduction

Chemistry


Atomic Structure


Chemical Bonds


Solutions


Reaction Rates


Chemical Equilibrium


Acids and Bases


Organic Chemistry

& Biochemistry


Biotechnology 101

Biology


Cell Biology


Genetics


Ecology


Evolution


Physiology

Investigation & Experimentation


It is what you make of it,
biotechnology helps you
make it great!


The California Science Standards (High School)

Introduction


What are the
current

trends in biotechnology education?


What are the
future

trends in biotechnology education?


What factors limit our ability to provide a solid
biotechnology foundation in grades K
-
12?


Funding for equipment


Teacher Knowledge and Experience


Time: Class Time, Prep Time

Biotechnology 101

Introduction


Animations

are
critical



they engage students and enable them to
visualize microscopic and/or abstract principles


Simulated labs and demos are helpful, but
hands
-
on labs

are
critical

to


Fully engaging students


Truly learning how to use equipment and perform techniques


Truly understanding the process of scientific discovery (scientific method)


Developing critical thinking skills


Developing students who are ready to enter the workforce or continue on to
study meaningful science at a college or university


Integration of
technical reading and writing

through the use of
journal
articles

and other primary and secondary sources is
critical

to developing
students who can understand the true process of science, manage their
own learning, evaluate scientific claims, communicate effectively, and
think critically


Biotechnology 101

Introduction


This

presentation will focus on

Animations

and other
online resources


Excellent resources for
hands
-
on labs

are available, but we will not have
time to look at these at this workshop


Amgen Bruce Wallace Biotechnology Lab Program

http://www.bwbiotechprogram.com

(Website includes links to many great biotech education lab support
organizations in California)


The Exploratorium (make your own equipment)


Bio
-
Rad and other vendors have excellent resources and materials
and will help train you


Science Literacy

How Do Scientists Communicate?




Presented by Kristin Majda




Sunday, 9:20 a.m., Room 211



Biotechnology 101

Resources for Teaching Genetics


Excellent

resources for understanding genetics are available from Cold
Spring Harbor’s online
DNA Learning Center (DNALC)


Genetics

is at the heart of
Biotechnology
, which aims to:


Develop therapies for genetic disorders, cancers, and other diseases in which
genetics plays a contributing role


Develop tissues for medical and research purposes (cloning, stem cells, tissue
engineering)


Use genetic profiles to differentiate among individuals and diagnose diseases


Enhance plants and other living organisms with useful genes


Understand the evolutionary history and relationships between species and
within species, both modern and extinct


Biotechnology 101

Resources for Teaching Genetics


Genetics and molecular biology involve abstract concepts


The DNA Learning Center (DNALC) includes

(
www.dnalc.org/resources/animations/)


Animations


Interactive websites


Curriculum development tools


Thematic lessons/units


Reference material


Biotechnology 101

www.dnalc.org/resources/animations/

Biotechnology 101

Real
-
time animations of
transcription, translation,
DNA replication, and many
biotechnologies

-

Many are downloadable

Stand
-
alone websites with
excellent resources for teaching
genetics and cellular and
molecular biology

Resources for Teaching Genetics


Genetic Basics (NIH Publication No. 01
-
662)

Free Guide from
National Institutes of Health.
http://www.nigms.nih.gov/


The Genes We Share with Yeast, Flies, Worms, and Mice

Free
guide from the Howard Hughes Medical Institute, Office of
Communications, 4000 Jones Bridge Road, Chevy Chase, Maryland,
20815
-
6789.

http://www.hhmi.org


Bruce Wallace Biotechnology Lab Program

Amgen Foundation
provides all materials and equipment (including reagents) for eight
comprehensive biotechnology labs.
http://www.bwbiotechprogram.com


Human Genome Project

http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

http://www.pbs.org/wgbh/nova/genome/program.html

http://www.pbs.org/wgbh/nova/genome/sequ_flash.html

Biotechnology in the Classroom

Resources for Teaching Genomics


Genomics

is the study of an organism's genome (entire set of genes)


The
Human Genome Project

is an international effort to map the entire
human genome based on DNA samples taken from a small group of
anonymous donors


http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml


The project began in 1990, rough draft of human genome announced in
2000, essentially complete genome was published in 2003 (two years early)


Broke the genome into segments approx. 150,000 base pairs long and then
ligated each segment into genetically engineered bacterial chromosomes
called BACs (bacterial artificial chromosomes). Inserted these vectors into
bacteria to amplify (make copies of) the DNA segments and then used
shotgun sequencing to determine the nucleotide sequence of each segment

Biotechnology 101

Resources for Teaching Genomics

What have we learned from the Human Genome Project?


The human genome contains 3.3 billion base pairs

(If expressed in units of computer data storage at 2 bits per base pair, there
would be 786 megabytes of raw data, which would be comparable to a fully
data loaded CD)


Almost all (99.9%) nucleotide bases are exactly the same in all people.


The human genome is estimated to contain 30,000 genes (much lower
than previous estimates of 80,000
-

140,000 genes).


Chromosome 1 has the most genes (2968), and the Y chromosome has
the fewest (231).


The average gene consists of 3000 bases, but sizes vary greatly, with
the largest known human gene being dystrophin at 2.4 million bases.


The functions are unknown for over 50% of discovered genes.



Biotechnology 101

Resources for Teaching Genomics

What have we learned from the Human Genome Project?


Genes appear to be concentrated in random areas along the genome,
with vast expanses of noncoding DNA between (other organisms'
genomes are more uniform, with genes evenly spaced throughout)


Stretches of up to 30,000 C and G bases repeating over and over often
occur adjacent to gene
-
rich areas, forming a barrier between the genes
and the "junk DNA." These CpG islands are believed to help regulate
gene activity.


Less than 2% of the genome codes for proteins.


Despite having more non
-
coding regions of DNA, humans have on
average three times as many kinds of proteins as the fly or worm
because of "alternative splicing" and chemical modifications to the
proteins resulting in the ability to produce different protein products
from the same gene.



Biotechnology 101

Resources for Teaching Genomics

Future goals of the Human Genome Project


Determine the function of all of genes


Identify all Single Nucleotide Polymorphisms (SNPs) and map them to
human diseases

Biotechnology 101

“The avalanche of genome data grows daily. The new challenge will be to use
this vast reservoir of data to explore how DNA and proteins work with each
other and the environment to create complex, dynamic living systems. Deriving
meaningful knowledge from the DNA sequence will define research through the
coming decades to inform our understanding of biological systems. This
enormous task will require the expertise and creativity of tens of thousands of
scientists from varied disciplines in both the public and private sectors
worldwide. Systematic studies of functional genomics will be the focus of
biological explorations in this century and beyond.”

Resources for Teaching Bioinformatics

Biotechnology 101


Bioinformatics

is the computational branch of molecular biology that
seeks to organize and make sense of all the genetic data being uncovered
(i.e. genomic sequences)

̵
Determine the location of genes on chromosomes, start and stop sites

̵
Predict the structure and function of resulting proteins

̵
Classify genes/proteins into families

̵
Determine evolutionary relationships between genes/proteins

̵
Determine molecular interactions within proteins and between two or
more proteins

̵
Determine/design potential receptors or ligands


Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Excellent explanations of

Bioinformatics principles,

tools, and techniques


Five progressive Lessons


Copyright allows

reproduction for

educational uses

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Lessons are supported

by a fictitious business

website that engages

students with role play

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

http://www.bscs.org/curriculumdevelopment/highschool/humangenome/bioinformatics/



Biotechnology 101

Resources for Teaching Bioinformatics


PyMOL

to visualize small molecules and macromolecules in 3D.

http://www.pymol.org/


Protein Data Bank
is a database that includes structural and
functional information about proteins, including the FASTA files
needed to display them in PyMOL.
http://www.rcsb.org/pdb


Jmol

is a simple tool for molecular visualization that has an online
gallery for easy access, with limited control over the appearance of
molecules.

http://molvis.sdsc.edu/fgij/index.htm


Biomolecular Explorer 3D

provides information about and 3D
images of relevent biological macromolecules right on the website.
http://www.umass.edu/molvis/bme3d/index.html


PredictProtein
provides analyses protein you input and predicts
structure.
http://www.predictprotein.org/


Biotechnology in the Classroom

Resources for Teaching Bioinformatics


PubMed

includes links to full text journal articles and other related
resources.
www.ncbi.nlm.nih.gov/entrez/


SWISS
-
PROT

protein database.
http://www.expasy.org/sprot/


SDSC Biology Workbench

allows scientists to search many protein
and nucleic acid sequence databases.
http://workbench.sdsc.edu


JCVI
-
CMR

(Comprehensive Microbial Resource) maintains
databases that include prokaryotic, plant, fungal, and parasitic
genomes.
http://cmr.jcvi.org/tigr
-
scripts/CMR/CmrHomePage.cgi


ORF Finder

scans a FASTA sequence for a segment of DNA to
determine potential open reading frames (sections that code for a
gene)
http://www.ncbi.nlm.nih.gov/gorf/gorf.html


Biotechnology in the Classroom

Resources for Teaching Bioinformatics


Proteomics Tools
-

http://www.expasy.ch/tools/


Glycan Structure Database
-

www.glycosuite.com


Lipid bank
-

http://lipidbank.jp/


3D Molecular Designs

-

Lends out molecular models for 2 weeks
www.3dmoleculardesigns.com

Biotechnology in the Classroom

Resources for Teaching Bioinformatics

Fold it

Protein folding game (http://fold.it/portal/info/science)


Biotechnology in the Classroom

More Free Tools & Resources


ELISA Tutorials/Animations




http://www.sumanasinc.com/webcontent/animations/content/ELISA.html


http://www.biology.arizona.edu/immunology/activities/elisa/technique.html


http://highered.mcgraw
-
hill.com/sites/0072556781/student_view0/chapter33/animation_quiz_1.html


Pregnancy Test Animation



use this website and a pregnancy test from the Dollar
Store to show your kids how antibodies are used to identify proteins in body fluids like
blood and urine

http://www.whfreeman.com/kuby/content/anm/kb07an01.htm


Microarray Tutorial/Animations


http://www.bio.davidson.edu/Courses/genomics/chip/chip.html


PCR Tutorial/Animation


http://www.maxanim.com/genetics/PCR/PCR.htm


http://www.youtube.com/watch?v=ZmqqRPISg0g


http://www.dnalc.org/resources/animations/pcr.html


DNA Sequencing Tutorial/Animation

http://www.biostudio.com/case_freeman_dna_sequencing.html

Biotechnology in the Classroom

More Free Tools & Resources


Recombinant DNA Tutorial/Animation


http://www.bioteach.ubc.ca/TeachingResources/Applications/GMOpkgJKloseGLampard2.swf


http://www.bioteach.ubc.ca/TeachingResources/Applications/GMOpkgJKloseGLampard2.swf


http://webapps.css.udel.edu/biotech/rDNA.html


Stem Cells


http://www.sumanasinc.com/scienceinfocus/sif_stemcells.html


http://www.dnalc.org/resources/animations/stemcells.html


Gel Electrophoresis Tutorial/Animation


http://www.dnalc.org/ddnalc/resources/electrophoresis.html


http://www.dnalc.org/resources/animations/gelelectrophoresis.html


http://learn.genetics.utah.edu/content/labs/gel/


Exploratorium Teacher Institute



4 week program in summer that teaches how to
make all kinds of “do it yourself” activities

(email annar@exploratorium.edu or call 415
-
561
-
0313)


McGraw Hill’s Biotechnology Animations


http://highered.mcgraw
-
hill.com/sites/0072437316/student_view0/chapter16/animations.html



Biotechnology in the Classroom

Biotechnologies for Your Classroom


Genetic Engineering


Recombinant DNA


Cellular Transformation


Gene Therapy


DNA Amplification

(PCR Method)


Separating and Identifying DNA


Gel Electrophoresis


DNA Sequencing

(Sanger Method)


DNA Microarrays


Epigenetics


Phylogenetics


Biotechnology 101


Proteomics


Immunoassays (ELISA)


Creating 3D Proteins


Protein Folding


Stem Cell Technology


Cloning


RNAi (gene silencing)


Cancer



Conclusion

Thank You for Coming





Kristin Majda

kmajda@yahoo.com

Biotechnology in the Classroom

Biotechnologies for Your Classroom

Biotechnologies
include methods to:


Cut (restriction enzymes), paste (ligation), and move DNA segments from one
chromosome to another (recombinant DNA) and/or one cell to another (transformation)
(Genetic Engineering)


Make many copies of DNA segments (amplification)


Identify individuals and/or diseases based on their unique DNA profiles (DNA
sequencing, DNA fingerprinting, immunoassays, bioinformatics)


Determine evolutionary relationships (phylogenetics) within and between species


Turn genes up (upregulation) and down (down regulation), or on (gene activation) and
off (gene silencing)


Grow cells (cell culture), manipulate stem cells to develop into specific tissue types
(differentiation), or manipulate differentiated cells to regress back to stem cells


Create genetically identical copies of organisms (cloning)

Biotechnology 101